Author: bugman
Date: Tue Oct 6 11:38:20 2009
New Revision: 9570
URL: http://svn.gna.org/viewcvs/relax?rev=9570&view=rev
Log:
Changes to the pcs.read() and rdc.read() user function interfaces.
Columns are now numbered from 1 - note this will break many things! The
spin_id_col is now accepted
and the spin_id arg is explained.
The docstrings have also been modified all over these user function classes
to replace
'identification string' with 'ID string'.
Modified:
1.3/prompt/pcs.py
1.3/prompt/rdc.py
Modified: 1.3/prompt/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/pcs.py?rev=9570&r1=9569&r2=9570&view=diff
==============================================================================
--- 1.3/prompt/pcs.py (original)
+++ 1.3/prompt/pcs.py Tue Oct 6 11:38:20 2009
@@ -43,7 +43,7 @@
Keyword Arguments
~~~~~~~~~~~~~~~~~
- id: The alignment identification string.
+ id: The alignment ID string.
"""
# Function intro text.
@@ -53,7 +53,7 @@
print(text)
# The argument checks.
- check.is_str(id, 'alignment identification string')
+ check.is_str(id, 'alignment ID string')
# Execute the functional code.
pcs.back_calc(id=id)
@@ -65,7 +65,7 @@
Keyword Arguments
~~~~~~~~~~~~~~~~~
- atom_id: The atom identification string.
+ atom_id: The atom ID string.
pipe: The data pipe containing the structures to extract the centre
from.
@@ -114,7 +114,7 @@
print(text)
# The argument checks.
- check.is_str(atom_id, 'atom identification string')
+ check.is_str(atom_id, 'atom ID string')
check.is_str(pipe, 'data pipe', can_be_none=True)
check.is_bool(ave_pos, 'average position flag')
@@ -132,7 +132,7 @@
pipe_to: The name of the pipe to copy the PCS data to.
- id: The alignment identification string.
+ id: The alignment ID string.
Description
@@ -169,7 +169,7 @@
# The argument checks.
check.is_str(pipe_from, 'pipe from', can_be_none=True)
check.is_str(pipe_to, 'pipe to', can_be_none=True)
- check.is_str(id, 'alignment identification string', can_be_none=True)
+ check.is_str(id, 'alignment ID string', can_be_none=True)
# Both pipe arguments cannot be None.
if pipe_from == None and pipe_to == None:
@@ -185,7 +185,7 @@
Keyword Arguments
~~~~~~~~~~~~~~~~~
- id: The alignment identification string.
+ id: The alignment ID string.
Examples
@@ -203,7 +203,7 @@
print(text)
# The argument checks.
- check.is_str(id, 'alignment identification string')
+ check.is_str(id, 'alignment ID string')
# Execute the functional code.
pcs.delete(id=id)
@@ -215,7 +215,7 @@
Keyword Arguments
~~~~~~~~~~~~~~~~~
- id: The alignment identification string.
+ id: The alignment ID string.
Examples
@@ -233,48 +233,63 @@
print(text)
# The argument checks.
- check.is_str(id, 'alignment identification string')
+ check.is_str(id, 'alignment ID string')
# Execute the functional code.
pcs.display(id=id)
- def read(self, id=None, file=None, dir=None, spin_id=None,
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None,
spin_name_col=None, data_col=None, error_col=None, sep=None):
+ def read(self, id=None, file=None, dir=None, spin_id_col=None,
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None,
spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None):
"""Read the PCS data from file.
Keyword Arguments
~~~~~~~~~~~~~~~~~
- id: The alignment identification string.
+ id: The alignment ID string.
file: The name of the file containing the PCS data.
dir: The directory where the file is located.
- spin_id: The spin identification string.
-
- mol_name_col: The molecule name column (this defaults to no column).
-
- res_num_col: The residue number column (the default is 0, i.e. the
first column).
-
- res_name_col: The residue name column (the default is 1, i.e. the
second column).
-
- spin_num_col: The spin number column (this defaults to no column).
-
- spin_name_col: The spin name column (this defaults to no column).
-
- data_col: The PCS data column (the default is 2).
-
- error_col: The experimental error column (the default is 3).
+ spin_id_col: The spin ID string column (an alternative to the mol,
res, and spin name and
+ number columns).
+
+ mol_name_col: The molecule name column (alternative to the
spid_id_col).
+
+ res_num_col: The residue number column (alternative to the
spid_id_col).
+
+ res_name_col: The residue name column (alternative to the
spid_id_col).
+
+ spin_num_col: The spin number column (alternative to the
spid_id_col).
+
+ spin_name_col: The spin name column (alternative to the
spid_id_col).
+
+ data_col: The RDC data column.
+
+ error_col: The experimental error column.
sep: The column separator (the default is white space).
+ spin_id: The spin ID string to restrict the loading of data to
certain spin subsets.
+
+
+ Description
+ ~~~~~~~~~~~
+
+ The spin system can be identified in the file using two different
formats. The first is the
+ spin ID string column which can include the molecule name, the
residue name and number, and
+ the spin name and number. Alternatively the mol_name_col,
res_num_col, res_name_col,
+ spin_num_col, and/or spin_name_col arguments can be supplied
allowing this information to be
+ in separate columns. Note that the numbering of columns starts at
one. The spin_id
+ argument can be used to restrict the reading to certain spin types,
for example only 15N
+ spins when only residue information is in the file.
+
Examples
~~~~~~~~
The following commands will read the PCS data out of the file
'Tb.txt' where the columns are
- separated by the symbol ',', and store the PCSs under the identifier
'Tb'.
+ separated by the symbol ',', and store the PCSs under the ID 'Tb'.
relax> pcs.read('Tb', 'Tb.txt', sep=',')
@@ -282,8 +297,8 @@
To read the 15N and 1H PCSs from the file 'Eu.txt', where the 15N
values are in the 4th
column and the 1H in the 9th, type both the following:
- relax> rdc.read('Tb', 'Tb.txt', spin_id='@N', res_num_col=0,
data_col=3)
- relax> rdc.read('Tb', 'Tb.txt', spin_id='@H', res_num_col=0,
data_col=8)
+ relax> rdc.read('Tb', 'Tb.txt', spin_id='@N', res_num_col=1,
data_col=4)
+ relax> rdc.read('Tb', 'Tb.txt', spin_id='@H', res_num_col=1,
data_col=9)
"""
# Function intro text.
@@ -292,7 +307,7 @@
text = text + "id=" + repr(id)
text = text + ", file=" + repr(file)
text = text + ", dir=" + repr(dir)
- text = text + ", spin_id=" + repr(spin_id)
+ text = text + ", spin_id_col=" + repr(spin_id_col)
text = text + ", mol_name_col=" + repr(mol_name_col)
text = text + ", res_num_col=" + repr(res_num_col)
text = text + ", res_name_col=" + repr(res_name_col)
@@ -300,14 +315,15 @@
text = text + ", spin_name_col=" + repr(spin_name_col)
text = text + ", data_col=" + repr(data_col)
text = text + ", error_col=" + repr(error_col)
- text = text + ", sep=" + repr(sep) + ")"
- print(text)
-
- # The argument checks.
- check.is_str(id, 'alignment identification string')
+ text = text + ", sep=" + repr(sep)
+ text = text + ", spin_id=" + repr(spin_id) + ")"
+ print(text)
+
+ # The argument checks.
+ check.is_str(id, 'alignment ID string')
check.is_str(file, 'file name')
check.is_str(dir, 'directory name', can_be_none=True)
- check.is_str(spin_id, 'spin identification string', can_be_none=True)
+ check.is_int(spin_id_col, 'spin ID string column', can_be_none=True)
check.is_int(mol_name_col, 'molecule name column', can_be_none=True)
check.is_int(res_num_col, 'residue number column', can_be_none=True)
check.is_int(res_name_col, 'residue name column', can_be_none=True)
@@ -316,6 +332,7 @@
check.is_int(data_col, 'data column', can_be_none=True)
check.is_int(error_col, 'error column', can_be_none=True)
check.is_str(sep, 'column separator', can_be_none=True)
+ check.is_str(spin_id, 'spin ID string', can_be_none=True)
# Execute the functional code.
pcs.read(id=id, file=file, dir=dir, spin_id=spin_id,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, data_col=data_col, error_col=error_col, sep=sep)
@@ -327,7 +344,7 @@
Keyword Arguments
~~~~~~~~~~~~~~~~~
- id: The alignment identification string.
+ id: The alignment ID string.
file: The name of the file.
@@ -353,7 +370,7 @@
print(text)
# The argument checks.
- check.is_str(id, 'alignment identification string')
+ check.is_str(id, 'alignment ID string')
check.is_str(file, 'file name')
check.is_str(dir, 'directory name', can_be_none=True)
check.is_bool(force, 'force flag')
Modified: 1.3/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/rdc.py?rev=9570&r1=9569&r2=9570&view=diff
==============================================================================
--- 1.3/prompt/rdc.py (original)
+++ 1.3/prompt/rdc.py Tue Oct 6 11:38:20 2009
@@ -43,7 +43,7 @@
Keyword Arguments
~~~~~~~~~~~~~~~~~
- id: The alignment identification string.
+ id: The alignment ID string.
"""
# Function intro text.
@@ -53,7 +53,7 @@
print(text)
# The argument checks.
- check.is_str(id, 'alignment identification string')
+ check.is_str(id, 'alignment ID string')
# Execute the functional code.
rdc.back_calc(id=id)
@@ -69,7 +69,7 @@
pipe_to: The name of the pipe to copy the RDC data to.
- id: The alignment identification string.
+ id: The alignment ID string.
Description
@@ -106,7 +106,7 @@
# The argument checks.
check.is_str(pipe_from, 'pipe from', can_be_none=True)
check.is_str(pipe_to, 'pipe to', can_be_none=True)
- check.is_str(id, 'alignment identification string', can_be_none=True)
+ check.is_str(id, 'alignment ID string', can_be_none=True)
# Both pipe arguments cannot be None.
if pipe_from == None and pipe_to == None:
@@ -122,7 +122,7 @@
Keyword Arguments
~~~~~~~~~~~~~~~~~
- id: The alignment identification string.
+ id: The alignment ID string.
Examples
@@ -140,7 +140,7 @@
print(text)
# The argument checks.
- check.is_str(id, 'alignment identification string')
+ check.is_str(id, 'alignment ID string')
# Execute the functional code.
rdc.delete(id=id)
@@ -152,7 +152,7 @@
Keyword Arguments
~~~~~~~~~~~~~~~~~
- id: The alignment identification string.
+ id: The alignment ID string.
Examples
@@ -170,7 +170,7 @@
print(text)
# The argument checks.
- check.is_str(id, 'alignment identification string')
+ check.is_str(id, 'alignment ID string')
# Execute the functional code.
rdc.display(id=id)
@@ -182,14 +182,14 @@
Keyword Arguments
~~~~~~~~~~~~~~~~~
- id: The alignment identification string.
+ id: The alignment ID string.
file: The name of the file containing the RDC data.
dir: The directory where the file is located.
- spin_id_col: The spin identification string column (an alternative
to the mol, res, and
- spin name and number columns).
+ spin_id_col: The spin ID string column (an alternative to the mol,
res, and spin name and
+ number columns).
mol_name_col: The molecule name column (alternative to the
spid_id_col).
@@ -207,7 +207,7 @@
sep: The column separator (the default is white space).
- spin_id: The spin identification string.
+ spin_id: The spin ID string to restrict the loading of data to
certain spin subsets.
Description
@@ -217,14 +217,16 @@
spin ID string column which can include the molecule name, the
residue name and number, and
the spin name and number. Alternatively the mol_name_col,
res_num_col, res_name_col,
spin_num_col, and/or spin_name_col arguments can be supplied
allowing this information to be
- in separate columns. Note that the numbering of columns starts at
zero.
+ in separate columns. Note that the numbering of columns starts at
one. The spin_id
+ argument can be used to restrict the reading to certain spin types,
for example only 15N
+ spins when only residue information is in the file.
Examples
~~~~~~~~
The following commands will read the RDC data out of the file
'Tb.txt' where the columns are
- separated by the symbol ',', and store the RDCs under the identifier
'Tb'.
+ separated by the symbol ',', and store the RDCs under the ID 'Tb'.
relax> rdc.read('Tb', 'Tb.txt', sep=',')
@@ -232,11 +234,12 @@
If the individual spin RDC errors are located in the file
'rdc_err.txt' in column number 5,
then to read these values into relax, type one of:
- relax> rdc.read('phage', 'rdc_err.txt', error_col=4)
- relax> rdc.read(id='phage', file='rdc_err.txt', error_col=4)
-
-
- If the RDCs correspond to the 'N' spin and other spins are loaded
into relax, then type:
+ relax> rdc.read('phage', 'rdc_err.txt', error_col=5)
+ relax> rdc.read(id='phage', file='rdc_err.txt', error_col=5)
+
+
+ If the RDCs correspond to the 'N' spin and other spin types such as
1H, 13C, etc. are loaded
+ into relax, then type:
relax> rdc.read('Tb', 'Tb.txt', spin_id='@N')
"""
@@ -260,10 +263,10 @@
print(text)
# The argument checks.
- check.is_str(id, 'alignment identification string')
+ check.is_str(id, 'alignment ID string')
check.is_str(file, 'file name')
check.is_str(dir, 'directory name', can_be_none=True)
- check.is_int(spin_id_col, 'spin identification string column',
can_be_none=True)
+ check.is_int(spin_id_col, 'spin ID string column', can_be_none=True)
check.is_int(mol_name_col, 'molecule name column', can_be_none=True)
check.is_int(res_num_col, 'residue number column', can_be_none=True)
check.is_int(res_name_col, 'residue name column', can_be_none=True)
@@ -272,7 +275,7 @@
check.is_int(data_col, 'data column', can_be_none=True)
check.is_int(error_col, 'error column', can_be_none=True)
check.is_str(sep, 'column separator', can_be_none=True)
- check.is_str(spin_id, 'spin identification string', can_be_none=True)
+ check.is_str(spin_id, 'spin ID string', can_be_none=True)
# Execute the functional code.
rdc.read(id=id, file=file, dir=dir, spin_id_col=spin_id_col,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, data_col=data_col, error_col=error_col, sep=sep,
spin_id=spin_id)
@@ -284,7 +287,7 @@
Keyword Arguments
~~~~~~~~~~~~~~~~~
- id: The alignment identification string.
+ id: The alignment ID string.
file: The name of the file.
@@ -310,7 +313,7 @@
print(text)
# The argument checks.
- check.is_str(id, 'alignment identification string')
+ check.is_str(id, 'alignment ID string')
check.is_str(file, 'file name')
check.is_str(dir, 'directory name', can_be_none=True)
check.is_bool(force, 'force flag')
r9570 - in /1.3/prompt: pcs.py rdc.py